Cancer is a disease with extensive histoclinical heterogeneity. Although conventional histological and clinical features have been correlated to prognosis, the same apparent prognostic type of tumors varies widely in its responsiveness to therapy and consequent survival of the patient.
New prognostic and predictive markers, which would facilitate an individualization of therapy for each patient, are needed to accurately predict patient response to treatments, such as small molecule or biological molecule drugs, in the clinic. The problem may be solved by the identification of new parameters that could better predict the patient's sensitivity to treatment. The classification of patient samples is a crucial aspect of cancer diagnosis and treatment. The association of a patient's response to a treatment with molecular and genetic markers can open up new opportunities for treatment development in non-responding patients, or distinguish a treatment's indication among other treatment choices because of higher confidence in the efficacy. Further, the pre-selection of patients who are likely to respond well to a medicine, drug, or combination therapy may reduce the number of patients needed in a clinical study or accelerate the time needed to complete a clinical development program (Cockett et al., Current Opinion in Biotechnology, 11:602-609 (2000)).
The ability to predict drug sensitivity in patients is particularly challenging because drug responses reflect not only properties intrinsic to the target cells, but also a host's metabolic properties. Efforts to use genetic information to predict drug sensitivity have primarily focused on individual genes that have broad effects, such as the multidrug resistance genes, mdr1 and mrp1 (Sonneveld, J. Intern. Med., 247:521-534 (2000)).
The development of microarray technologies for large scale characterization of gene mRNA expression pattern has made it possible to systematically search for molecular markers and to categorize cancers into distinct subgroups not evident by traditional histopathological methods (Khan et al., Cancer Res., 58:5009-5013 (1998); Alizadeh et al., Nature, 403:503-511 (2000); Bittner et al., Nature, 406:536-540 (2000); Khan et al., Nature Medicine, 7(6):673-679 (2001); and Golub et al., Science, 286:531-537 (1999); Alon et al., P. N. A. S. USA, 96:6745-6750 (1999)). Such technologies and molecular tools have made it possible to monitor the expression level of a large number of transcripts within a cell population at any given time (see, e.g., Schena et al., Science, 270:467-470 (1995); Lockhart et al., Nature Biotechnology, 14:1675-1680 (1996); Blanchard et al., Nature Biotechnology, 14:1649 (1996); U.S. Pat. No. 5,569,588).
Recent studies demonstrate that gene expression information generated by microarray analysis of human tumors can predict clinical outcome (van't Veer et al., Nature, 415:530-536 (2002); Sorlie et al., P. N. A. S. USA, 98:10869-10874 (2001); M. Shipp et al., Nature Medicine, 8(1):68-74 (2002): Glinsky et al., The Journal of Clin. Invest., 113(6):913-923 (2004)). These findings bring hope that cancer treatment will be vastly improved by better predicting the response of individual tumors to therapy.
The epidermal growth factor receptor (EGFR) and its downstream signaling effectors, notably members of the Ras/Raf/MAP kinase pathway, play an important role in both normal and malignant epithelial cell biology (Normanno et al., Gene 366, 2-16 (2006)) and have therefore become established targets for therapeutic development. Whereas the anti-EGFR antibody cetuximab and the EGFR small molecular tyrosine kinase inhibitors (TKIs) gefitinib and erlotinib have demonstrated activity in a subset of patients (Baselga and Arteaga, J. Clin. Oncol. 23, 2445-2459 (2005)), their initial clinical development has not benefited from an accompanying strategy for identifying the patient populations that would most likely derive benefit. The hypothesis that only a relatively small number of tumors are “EGFR-pathway dependent” and therefore likely to respond to EGFR inhibitors might explain the limited clinical activity that is observed with this class of therapeutics. For example, in patients with refractory metastatic colorectal cancer clinical response rates with cetuximab consistently range from 11% in a monotherapy setting to 23% in a combination setting with chemotherapy (Cunningham et al., N. Engl. J. Med 351, 337-345 (2004)). To date, significant efforts have been focused on elucidating the mechanisms of sensitivity or resistance to EGFR inhibition, particularly through evaluation of EGFR protein expression, kinase domain mutations, and gene copy number.
While relative protein expression of the EGFR as measured by immunohistochemistry (IHC) has been demonstrated in many solid tumors (Ciardiello and Tortora, Eur. J. Cancer 39, 1348-1354 (2003)), no consistent association between EGFR expression and response to EGFR inhibitors has been established. Clinical studies of cetuximab in a monotherapy setting and in combination with irinotecan in patients with mCRC failed to reveal an association between radiographic response and EGFR protein expression as measured by IHC (Cunningham et al., N. Engl. J. Med 351, 337-345 (2004); Saltz et al., J. Clin. Oncol. 22, 1201-1208 (2004)). Furthermore, clinical responses have been demonstrated in patients with undetectable EGFR protein expression (Chung et al., J. Clin. Oncol., 23, 1803-1810 (2005); Lenz et al., Activity of cetuximab in patients with colorectal cancer refractory to both irinotecan and oxaliplatin. Paper presented at: 2004 ASCO Annual Meeting Proceedings; Saltz, Clin Colorectal Cancer, 5 Suppl. 2, S98-100 (2005)). In comparison, clinical studies of erlotinib in NSCLC patients and gefitinib in ovarian cancer did demonstrate an association between EGFR expression, response, and survival (Schilder et al., Clin. Cancer Res., 11, 5539-5548 (2005); Tsao et al., N. Engl. J. Med., 353, 133-144 (2005)). The presence of somatic mutations in the tyrosine kinase domain, particularly in NSCLC has been extensively described (Janne et al., J. Clin. Oncol., 23, 3227-3234 (2005)). In both preclinical and clinical settings, these mutations are found to correlate with sensitivity to gefitinib and erlotinib but not to cetuximab (Janne et al., J. Clin. Oncol., 23, 3227-3234 (2005); Tsuchihashi et al., N. Engl. J. Med., 353, 208-209 (2005)). In addition, the lack of EGFR kinase domain mutations in CRC patients suggests that such mutations do not underlie the response to cetuximab. EGFR gene copy number has also been evaluated as a potential predictor of response to EGFR inhibitors. Clinical studies of gefitinib demonstrated an association between increased EGFR copy number, mutational status, and clinical response (Cappuzzo et al., J. Natl. Cancer Inst., 97, 643-655 (2005)). A similar association was identified in a small number of patients treated with the anti-EGFR monoclonal antibodies cetuximab and panitumumab (Moroni et al., Lancet Oncol., 6, 279-286 (2005)). Additional potential predictive biomarkers have also been evaluated. For example, in glioblastoma patients, a significant association between co-expression of EGFRvIII and PTEN and response to EGFR small molecule inhibitors was found (Mellinghoff et al., N. Engl. J. Med., 353, 2012-2024 (2005)).
The anti-tumor activity of cetuximab has been attributed to its ability to block EGFR ligand binding and ligand-dependent EGFR activation. Clinical activity of cetuximab has been shown in multiple epithelial tumor types (Bonner et al., N. Engl. J. Med., 354, 567-578 (2006); Cunningham et al., N. Engl. J. Med., 351, 337-345 (2004)), however responses continue to be seen in only a fraction of patients. Previous attempts to identify predictors of sensitivity or resistance as described above have focused on specific biomarkers rather than using genomic discovery approaches. In addition, RNA-, DNA- and protein-based markers have rarely been examined in the same patient population in a single study, making comparisons challenging.
Biomarkers useful for determining sensitivity to EGFR modulators have been described in published PCT applications WO2004/063709, WO2005/067667, and WO2005/094332.
Needed are new and alternative methods and procedures to determine drug sensitivity in patients to allow the development of individualized genetic profiles which are necessary to treat diseases and disorders based on patient response at a molecular level.